Analysis of Full-Length Human Immunodeficiency Virus Type 1 Genome Reveals a Variable Spectrum of Subtypes B and F Recombinants in São Paulo, Brazil

Filho, Dercy José de Sá; Sanabani, Sabri Saeed; Diaz, Ricardo Sobhie; Munerato, Patrı́cia; Brunstein, Adriana; Fusuma, Erika Etsuko; Sabino, Éster Cerdeira; Janini, Luiz Mário

doi:10.1089/aid.2005.21.145

Cited by 43 publications

(56 citation statements)

References 21 publications

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“…In Brazil, subtypes B, C, F, and recombinants cocirculate. In Sao Paulo, subtype B accounts for 90% of the infections, and subtype F for 4% [20]. B/F recombinants, some of which share common breakpoints in the pol gene but differ in their structure in other genes, were also found, in concordance with previous studies that found several B/ F URFs but failed to detect a CRF in Brazil.…”

Section: South America and The Caribbeansupporting

confidence: 89%

HIV diversity, molecular epidemiology, and the role of recombination

Kijak

McCutchan²

2005

Curr Infect Dis Rep

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The magnitude of the HIV pandemic and its extensive genetic variation may earn it a unique place among infectious agents. A high mutation rate and a rampant recombination are driving HIV's evolution. Nine subtypes and a variety of recombinant forms of HIV now exist. The source of recombinant forms is the multiple infection of target cells, which becomes highly significant when individuals become infected with two or more divergent strains. In the current paper, we re-examine the role of dual infection and recombination in the generation of HIV-1 diversity, both in individuals and on a global scale. The current molecular epidemiology of HIV-1 is reviewed, emphasizing the latest reports from regional epidemics.

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Section: South America and The Caribbeansupporting

confidence: 89%

HIV diversity, molecular epidemiology, and the role of recombination

Kijak

McCutchan²

2005

Curr Infect Dis Rep

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“…Recombination breakpoints have been found in nucleotide region 230-330, i.e., in the sequence that folds to the predicted structure, between the pol gene sequences from different subtypes, such as between subtypes A and B, A and D, and B and D, as well as between B and F (Quarleri et al 2004;Yang et al 2004;Sa Filho et al 2005). However, the existence of breakpoints in this region is insufficient to define a recombination hot spot.…”

Section: Role Of the Rna Secondary Structurementioning

confidence: 99%

Evidence of a novel RNA secondary structurein the coding region of HIV-1 pol gene

Wang

Barr²,

Guo³

et al. 2008

RNA

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RNA secondary structures play several important roles in the human immunodeficiency virus (HIV) life cycle. To assess whether RNA secondary structure might affect the function of the HIV protease and reverse transcriptase genes, which are the main targets of anti-HIV drugs, we applied a series of different computational approaches to detect RNA secondary structures, including thermodynamic RNA folding predictions, synonymous variability analysis, and covariance analysis. Each method independently revealed strong evidence of a novel RNA secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, A, B, and C. First, RNA folding calculations by mfold and RNAfold both predicted the secondary structure with high confidence. Moreover, the same structure was predicted in a diverse set of reference sequences in HIV-1 group M, indicating that it is conserved across this group. Second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 HIV-1 subtype B sequences from clinical samples. Third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems A and B. Finally, this structure was validated experimentally using selective 29-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation.

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“…Studies on the env and pol regions indicate co-circulation of subtypes B (62.5-82.9%), F (8-18%) and C (3-45%) (Bongertz et al, 2000;Brindeiro et al, 2003). Evidence of B/F and B/C recombinants involving the env, gag, nef and pol regions have been reported in southeast Brazil (Guimaraes et al, 2002;Sa Filho et al, 2005;Sanabani et al, 2006). There are regional differences in the pattern of HIV-1 subtypes.…”

Section: Introductionmentioning

confidence: 99%